Research workbench
Structure of astrotactin-2, a conserved vertebrate-specific and perforin-like membrane protein involved in neuronal development
Analyse Structure of astrotactin-2, a conserved vertebrate-specific and perforin-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J69
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Astrotactin-2
- UniProt
- O75129
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Astrotactin-2 | protein | 248 | 26% helix, 25% strand | O75129 |
| B | Astrotactin-2 | protein | 255 | 29% helix, 26% strand | O75129 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.67 | 0.92 | 16 | empty |
| 2 | 427 | 0.65 | 0.78 | 45 | empty |
| 3 | 74 | 0.39 | 0.78 | 17 | empty |
| 4 | 91 | 0.37 | 0.75 | 19 | empty |
| 5 | 65 | 0.37 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 453 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5J69 · Structure of Astrotactin-2, a conserved vertebrate-specific and perforin-like membrane… · the same entry in another collection · chain A against A, TM-score 1.00
- O75129 · AlphaFold monomer V2.0 prediction for astrotactin-2 (O75129) · a predicted model of the same protein · chain A against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O75129
- Elsewhere: RCSB PDB 5J69 · PDBe 5J69 · UniProt O75129
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